The HierarchicalGroups.orthoxml file contains all splicing variants as individual genes in the header part. As only one (the infered main isoform) will appear in any orthology relation, tools like pyham will list the alternative isoforms as species specific gene gains, which is wrong.
The HierarchicalGroups.orthoxml file contains all splicing variants as individual genes in the header part. As only one (the infered main isoform) will appear in any orthology relation, tools like pyham will list the alternative isoforms as species specific gene gains, which is wrong.